Steps to reproduce:
1. Download and enable the UUID and References modules.
2. Add a node reference field to fieldable panel pane entities.
3. Create a fieldable panel pane, and add a reference to a node.
4. Place the fieldable panel pane inside a panel.
When you look at the panel, the referenced node will not be displayed.
(The same thing would happen with Entity Reference module also, by the way, except there's currently another bug in the UUID module's integration with Entity Reference which cancels this one out.)
The cause of the bug is that Fieldable Panels Panes is using entity_uuid_load() to load entities by UUID, but that's the wrong function. What that function does is load an entity in which all local IDs have been replaced by UUIDs. But when Drupal goes to render a node reference field, it won't know what to do with the UUIDs, so it's not able to find the referenced node.
A patch is coming up.